


song for the waiting

by piratesails



Category: Once Upon a Time (TV)
Genre: Alternate Universe - Modern Setting, Alternate Universe - Spies & Secret Agents, F/M, Fluff and Angst, it's mainly just used as a character trait, the first chapter of this now exists in like four different places, you will however find a lot of pining, you won't find a lot of espionage in this
Language: English
Status: Completed
Published: 2020-12-15
Updated: 2020-12-19
Packaged: 2021-03-10 21:15:56
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings, No Archive Warnings Apply
Chapters: 3
Words: 4,497
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/28083792
Author URL: https://archiveofourown.org/users/piratesails/pseuds/piratesails
Summary: She hates hiding out in Storybrooke, not being on her feet and in the middle of some fight or the other. It’s all she knows. But some part of her likes the quiet that comes with sitting by the ocean, the ease with which she tells the handful of people she talks to her real name, the odd comfort when Killian falls asleep on her sofa after a long day of work.Of course, Killian Jones had never been a part of her plan.Spy/Civilian AU.
Relationships: Captain Hook | Killian Jones/Emma Swan
Comments: 37
Kudos: 87





	1. Chapter 1

**Notes for the Chapter:**

> me, writing captain swan in 2020? it's more likely than you think!
> 
> back in 2017, I wrote a scene for a prompt challenge, referred to it as my “angsty spy au” and then did jackshit about it. yesterday, I found an expanded version of it in my google docs, was hit by some inspiration, and decided to polish it and finish it up. if you follow me anywhere, you'll have read this first chapter already, but fret not, there's two more new ones to wrap this up!

Emma knows how to compartmentalize. She keeps her work life separate and her personal life separate, knowing never to let the two even begin to touch. It’s the only way to go when you’re working as a spy for a secret organisation.

She keeps late night missions in one place. She keeps her grocery list in another. She keeps her extensive knowledge of hand to hand combat in one place. And Killian Jones, neighbour, and the only friend she may have ever had, in another.

She’d moved into the small seaside town when her mission in Austria had ended, opting to take some time off from work while still assisting in researching for them. Technically, it was desk duty. And technically, she hadn’t “opted” for it more than it had been “forced” upon her by Ingrid when she got shot during her last job. It wasn’t  _ that _ fatal, and Pan got away, which meant that she was sent to Nowhere, Maine, for her safety after her identity had been compromised.

Meaning, she has to work extra hard to track him from her unrecognizable corner of the world.

She hates it, not being on her feet and in the middle of some fight or the other. It’s all she knows. But some part of her likes the quiet that comes with sitting by the ocean, the ease with which she tells the handful of people she talks to her real name, the odd comfort when Killian falls asleep on her sofa after a long day of work.

Killian Jones hadn’t been a part of her plan. Not at all. Her aim was to stay underground for a few months, nothing more than a year, and then get back out there. Now though, every time she thinks of leaving, she thinks of leaving him. Which basically means she tries as hard as possible to not think about leaving even though she knows it’s inevitable.

“The pizza should be here soon,” Killian announces as he comes out of his room, sweatpants hanging low and threadbare shirt stretching across his chest. She tells herself she doesn’t stare, but she’s a trained bullshitter, so, whatever. Sue her.

“Great,” she replies, attempting to focus her attention back on Netflix.

Killian sits down next to her, his body pressing against hers from hip to knee. She doesn’t know how this man weaseled his way into her life, but now she can’t imagine anything else besides having him around. He takes the remote from her hand to stop her mindless scrolling just as there’s a knock on the door.

She gets up before he can, and grabs the cash off the table before opening the door. She’s already paid and has the pizza in her hand when she hears the heavy shuffle of boots at the end of the hallway, close to her apartment door. Discreetly, Emma peeks her head out and immediately feels her heart speed up at the sight of two burly guys she’s pretty sure work for Pan. They’ve all got that same just-burst-out-of-prison look. 

And they’ve found her. 

She knows it was only a matter of time until her real life caught up with her but  _ fuck _ .

She manages to move back in quickly without drawing attention to herself. She hears them banging at her door, and she knows that any minute now they’ll break through it and realize she isn’t inside. Emma doesn’t have much of a choice at this point.

“What’s wrong, love?” Killian asks, twisting to watch her with a concerned look.

“I— I need to go.”

“Come again?”

“I need to get out of here, I—” 

She drops the box on the kitchen counter and makes a beeline for the fire escape. Killian’s up and catching her elbow before she can reach for the window.

“Swan, what the bloody hell has gotten into you?”

“I’m sorry, I need to go. If people come by here looking for me, tell them you don’t know who I am, I can’t have you involved in this. I can’t explain right now, but I really need you to trust me.” She gets it out hurriedly, and feels her voice shake more with every word.

“Emma, if you’re in some kind of trouble, I can—”

“You can’t do anything, just trust me, okay?”

Killian nods even though he looks like he wants nothing more than to argue. “Where are you going?”

“I don’t know, and I don’t know when I’ll see you again, but—” she breathes in heavily and does what she’s been stopping herself from doing for months and surges forward to kiss him. He melts into her immediately and gives as good as he gets. She wishes so hard that it didn’t feel like a goodbye but it does. She breaks away and has to remind herself to breathe when she sees the desperate expression on his face.

There’s a loud shout from one of the men outside and a crashing sound, no doubt in frustration, and she knows her time is running out.

“Go,” Killian tells her, releasing his hold on her. “And Swan, please be safe.”

She nods and is halfway out the window when she says with a weak smile and a determined set to her brows, “I’ll find you, Killian, I promise.”

“I’ll hold you to that, love.”

She lets herself look at him one last time before she turns and jumps out the window.

**Notes for the Chapter:**

> comments are always appreciated <3


	2. Chapter 2

**Notes for the Chapter:**

> it makes me v happy to see everyone's enthusiasm on me continuing this little fic; it is wholly silly and self indulgent but it has felt so good to revisit this part of myself and be immersed in fandom again

Emma spends what feels like a lifetime trying to comprehend the basics of Icelandic before giving up entirely, becomes enthralled with the magic of the streets of Istanbul, and barely makes it through two days in London before the accents of the people around her start hitting too close to home. 

Before she knows it, she's gotten through half of Europe, while her head’s still stuck in a small apartment in Maine, with its teal accents and its ever present smell of spice and the sea.

It's not like she isn't trying to focus on the mission at hand — which, in Ingrid’s words, is simply to “keep your head down and stay alive until we figure it out” —, it's merely that the mission at hand is a stupid one. Emma needs to find Pan, give him what he deserves (read: nothing good), and when the smoke clears afterwards, maybe she'll catch a flight to New England for nostalgia’s sake. It isn't her goal, it isn't _why_ she's pushing through and gearing herself up for a fight with a total raging psycho. Not at all. 

She's set herself up in a small studio in Nice when Ingrid calls her, finally, after nine weeks of radio silence. 

Pan has taken refuge somewhere in Kadavu Island, has managed to figure out a way to keep operating, sticking his slimy little hands in everywhere, from where he’s sitting. She wants to drown him in the South Pacific Ocean. 

She’s already shoving clothes into a bag as soon as Ingrid tells her where he is, the burner phone pressed uncomfortably between ear and shoulder, ready to take the next flight out when she’s shaken out of her haphazard planning. 

“You’re not going.”

She stands up straight and glares at the wall. “What do you mean I’m not going? Of course I’m going.”

“Emma, I know you’ve got this personal vendetta against Pan—“

“I don’t have a personal _anything_.”

“—but we’re going to keep monitoring him. It’s not a good idea to strike right now. We’re short of agents—“

“I’m literally at your disposal!”

“I’m not talking about you, and even if I was, you’re never going to go in there alone.” Emma makes a sound of annoyance, interrupting her. Again. Ingrid sighs. “I need you to keep doing what you’re doing. We have intel that he’s going to make a move in a few months’ time, and that’ll be the perfect time to execute our takedown. I’ll be in touch.”

“Ingrid, I can do this. If you’d just—“

“Look, Emma, you’re my best agent. Don’t tell anyone I said that, but you are. They’re already after you, and if I send you in there now, guns blazing and without an exit strategy, you’re not going to come back. You have to trust me.”

She does, which is the problem. Because then it’s months of new apartments, of fake names, of changing her hair colour and her accent. Of hiding out in a farmhouse in Multan, spending nights at a dive bar in Hanoi, being a little too caught up in how familiar the blue of the water in the fishing village of Kampong Phluk looks, cutting off almost all of her hair when the heat of Manila gets too much to deal with. 

It feels like she’s gone through several different lifetimes, several different versions of a false reality, before it happens. Before they pull off their infiltration of his inane setup, the skill and quantity of her team no match for his own. Before she’s finally in front of Pan, gun pointed straight at his chest, his face scrunched up like a petulant child. She’s bleeding from somewhere below her shoulder and her knuckles are screaming in pain from colliding with Pan’s cheekbone but there’s no part of her that cares. Especially when he’s finally flown into their holding facility, and they’ve done it; they’ve caught one of the most notorious underground ring leaders of the last decade.

It takes over a year of recovery and physiotherapy (she really needs to stop getting shot, it’s becoming a pain in her ass), and of carefully dismantling Pan’s entire network with her team in New York, before she’s finally dusted her hands of the whole job. The second she turns her report in, she feels a surge go through her body. Ingrid tells her she’s free to take some time off, and she gets as far as her apartment before the adrenaline wears off and the panic settles in.

Because it’s been almost two years now since she’s seen Killian Jones. She has no doubt that unlike her, his life must have moved on — forward, without her. So what if she still remembers how perfectly she’d fit into his arms when he’d hug her? How he’d make her laugh after she’d mention bits of her true and shitty past? How good he was at darts, but how terrible he was at charades? How he’d keep her favourite flavour of coffee creamer in his apartment just for her? How his lips felt on hers?

That didn’t have to mean anything, did it?

It didn’t, she decides.

She lies to herself about it for several months. Gets tired of New York, then of Minnesota, of Texas, even of Oregon. She’s in Boston, under the harsh light of a convenience store in the middle of the night, staring at a box of instant mac and cheese — the exact same one that Killian had refused to let her buy once, telling her that he could cook it better from scratch — when she stops lying. 

It’s funny that she doesn’t think twice about going up against people who could kill her in an instant, but that it has taken her this long to muster up the courage to get in her car and drive across the town line of Storybrooke. There’s a feeling that has been swelling in her chest since she’d kissed him — maybe even since before that. It’s got a lot to do with the way Killian would grin at her, would tuck her into his side when it would get too cold out, would hum a lullaby when she’d frustratedly fling herself onto the couch after getting nowhere with research.

That one tune he’d hum has been haunting her for years, making an appearance in parts of her dreams, pushing itself to the forefront of her thoughts on any given day. She has no idea where it’s from but she’s memorised it, hums it to herself when she can’t relax. Which has been often.

And that feeling that has made home in her body, it’s something about care, and want, and— 

She grips the wheel a little harder as she takes a right into his street, and tells herself that under no circumstances is she allowed to throw up when she gets to his door. 

She hasn’t felt capital-L _Love_ in years, so it isn’t until she’s standing there, inches away from the entrance of his apartment, that she finally recognizes it. In all its stupid, overwhelming glory. The same Love that flung her from one city to the next, urging her to come back to this little seaside town in Maine. 

Taking down Pan really was easier than this. She’d laugh about it if her stomach wasn’t twisting itself in knots. She takes a deep, steadying breath, raises her hand, and knocks.

**Notes for the Chapter:**

> I had a lot of fun writing this chapter, so drop me a comment on your thoughts, and come say hi on [tumblr](http://piratesails.tumblr.com/) <3


	3. Chapter 3

Killian Jones used to be a man of habit, his Navy training enforcing a certain way of living into him. He'd thought that a life without order was a life wasted in scrambled chaos. 

That was before his brother died, before everything he knew was turned in over its head. Before he was forced to pick himself up, drunk and disheveled, off of the floor of his kitchen (alternatively, bathroom) in the middle of the night.

He’d developed an appreciation for a more easy-going lifestyle after his recovery. Routines were still good for him, and even now, he still hasn’t been able to shake off the habit of waking up with the sun. But, essentially, he didn’t have a rod up his arse any longer. It was easier to maintain contentment and a vague appreciation for being alive when he wasn’t giving himself a hard time over his lack of control.

It was a happy middle. 

He thought so, anyway, until the fateful morning he’d shared an elevator ride with Emma Swan. He doesn’t think he’d actually known  _ happy _ until she’d smiled at him. That, and every subsequent run-in with her that eventually led to Killian memorizing the way her face would light up when he’d order her extra onion rings, or the way she’d sometimes rest her head on his shoulder when they’d watch a movie together. 

He’d had this plan, or at least, two-thirds of it — it had involved renting a boat, and a speech that was only half written down, and a lot of rum for the both of them. It was, by all accounts, chaos. But he’d figured he still had time to figure out what he would say and how he would say it. Because it was of vital importance that he tell Emma Swan just how he felt about her.

That was before she kissed him something fierce and jumped down the fire escape. That was over two years ago, and since then he’s been nursing her parting promise and a heavy heart. He’s stayed away from nursing bottles. That last one hasn’t been easy, but his meetings help, even if everyone around town had spent weeks asking him where Emma had disappeared to.

He hadn’t had an answer. Still doesn’t. 

Still isn’t sure how he’s supposed to get on with his life when the woman he’s decidedly in love with is somewhere, possibly still in trouble, and not pulling him by the back of his shirt so he messes up his dart throw. 

He doesn’t even know if he knows who she is, really. Those men that came in looking for her that wretched day seemed adamant on finding her and he doesn’t give a crap about anything else other than that she’s safe wherever she is.

(Even if he wishes, selfishly, that it was with him.) 

Since she left, he’s worked longer hours than necessary, taken on tasks that, as harbor master, he should be delegating. But it gives his hands something to do, something that reminds them that they are capable of doing other things besides holding Emma. The time after her has sort of blurred together and it seems he’s always halfway between worry and despair. He still finds it hard to come back to his apartment most days, never realizing before just how large it seems when it’s just him in it. And despite the hours he works, sleep hardly ever comes easy. 

When he hears the knock on his door at half past two in the morning, he thinks it’s just his imagination. He’s pushing the tangle of sheets off his legs when it sounds again.

He’s not in the best of places, running on barely any sleep, both his mind and his heart a mess, and he pulls the door open with a fierce force, ready to bark at whoever has decided that this is an acceptable time to be calling upon him. 

And there, against his wildest bloody dreams, stands Emma Swan.

Her hair is short now. Still a striking blonde shade and curled to perfection, but stopping just short of her chin. 

Killian can’t seem to bring himself to think of much else besides this one fact. Not that she is here, standing outside his front door, after years have gone by. Not that he has been praying to one deity or another every given hour that she finds her way back to him, unscathed and alive.

“Hi,” she says meekly, a smile starting at the edge of her mouth. It’s hardly appropriate to focus on her mouth. Killian shakes his head because surely he’s dreaming. “I’m sorry I woke you, I was just kind of running off adrenaline and the heating in my car is temperamental so I didn’t think it was a good idea to wait till morning—”

He propels himself forward and pulls her into his arms. It effectively stops her rambling and speeds up his heart rate. Her hands come around him immediately, and he tightens his hold on her. He is definitely not dreaming.

“Swan,” he exhales, and feels her press her nose into his throat. “I’m so glad you’re alright.”

“This place looks exactly the same,” she notes wistfully as he tugs her into the apartment. 

“Your hair is shorter,” comes his immediate reply.

Her hand shoots up at once to tug at the ends of her curls. “Yeah, I— it was way shorter than this because I couldn’t take the heat, but it’s growing out now.”

“The heat? Just where were you, Swan?”

She breathes in slowly, exhales. Her eyes dart between his, and there’s some kind of pleasantness in realizing that all this time, he’s been remembering the shade of green of her eyes perfectly. “It’s a long story,” she says. “You want some tea?”

He nods, and takes over the task of making it as soon as she steps into his kitchen. She gives him a small smile and gods, he’s missed her. More than he ever thought was possible. His pulse still refuses to come down to a steady pace when she starts telling him the story, about who she really is, where she really works. There’s international criminals, and bullet wounds, and hopping from cities to countries to continents. It’s like he’s listening to the plot of a Bond movie rather than hearing about the life of his closest friend, of the woman he’s crazy about. 

It takes five mugs of tea between the both of them, and several detours when he interrupts with questions and makes disconcerting noises every time she mentions how close she had been to being seriously injured, before there’s silence and she’s carefully watching him. There’s a hint of trepidation in her eyes and when he stays quiet for what must be too long, she speaks up again.

“I’m sorry I lied to you. At first it was just because it’s the nature of my job, but then it was because I wanted to—  _ had _ to protect you.”

“How much of it was a lie?” he asks. Because he’s still processing, and can’t get over the fact that she’s sustained far more life-threatening wounds than he himself had seen when he was in the Navy. 

“The stuff about my job, things like that. Most of what I told you about my past is true, I really was abandoned on the side of the road. Don’t think I could make that shit up if I tried.” 

He wants to hold her. Never let her go. “Your name?”

She shakes her head. “Emma Swan. I could show you my birth certificate if you want.”

He huffs in amusement. “I believe you, love.”

She smiles too, and he finally catches a wink of her dimples. How on earth did he survive so long without her?

And then he asks, because he’s past making plans and being content and making up stories in his head. And because he’s a bloody desperate man. “What about that kiss? Was that real?”

Her throat works a swallow and she looks anywhere but directly at him. She’s already nestled into one corner of his couch, otherwise he thinks she’d be backing up against a wall. He notices her eyes catch on to the window, and then she replies, “I didn’t have the best life before I started working, as you kind of know. The organization is full of people like me, people who have nothing to live for. It’s what makes it so easy to put ourselves in the dangers that we do.” She takes a deep breath and looks at him. “After I met you, I couldn’t put myself in the same category anymore, because for once, I had something worth losing.”

It’s everything he never thought he’d hear. Not in the last two years anyway. Of course he had hoped but—

He moves towards her slowly, carefully prying the mug out of her hands and placing it on the coffee table. Taking both her hands in his, he swipes his thumbs over her knuckles. 

“I had hoped you’d find me like you’d said, but I still tried to look for you. I scoured the internet, got David to look you up in his sheriff’s database and exhaust every professional contact of his, even hired a private investigator,” he admits. “There has been nothing I have wanted more than to see you again.”

She squeezes his hands, looking down at where they’re joined and resting in her lap.

“Swan, why did you come back?” 

“Because I said I would.”

“Emma.” 

She looks at him then, tightens her grip just a little more. “Because nothing made sense without you.”

It’s all he needs before he’s kissing her. He pushes both hands into her hair, and she pulls at his waist to bring him closer. He feels like someone has finally breathed life into him, several months’ worth of hurt and confusion and sadness dissolving into thin air right in front of him as Emma Swan tugs at his hair to get a better angle to deepen the kiss. He catalogues the soft moan that escapes her for later as he pulls her into his lap.

“I missed you so bloody much, Swan.” She’s breathing hard, forehead pressed against his, and at his words, she leans down to press a featherlight kiss against the corner of his mouth.

“Me too.”

“Things have not been the same since you left,” he tells her sincerely. 

“Except the apartment.”

He can’t help his laughter, kisses her again and again and again until the laughter’s bubbling out of her, too, their teeth clashing clumsily because they can’t stop smiling. His heart feels like it could burst from happiness.

“Except the apartment,” he confirms.

She settles onto his lap, tracing the curve of the shell of his ear with her fingers. Killian can’t stop staring at her, and even if he could, he doesn’t think he would want to. Emma Swan is a vision, all flushed cheeks and mussed hair and a smile lingering on her lips.

He doesn’t want to ask her what he does next, but knowing what he does now, it may be simpler to manage expectations. “Not that I’m not enjoying this, but indulge me for a moment. How long do we have before you’re off to save the world again?”

She brushes off his compliment, and he is too aware of the fact that he will never stop telling her just how bloody brilliant she is. 

“I was thinking,” she starts after a moment, “that finishing what may be the biggest job of my career and being shot twice are probably enough reasons for me to ask for assignments that are more remote.”

His fingers draw mindless patterns on the small of her back. “I’m not sure I’m following.”

“I mean that no matter where I went, Storybrooke was the only place I wanted to be.” She punctuates her sentence with a tug at the tip of his ear. “And I want to stay.” 

Here.  _ With him.  _

“Love, there is absolutely nothing more I would like than for you to stay. But what of your identity? And didn’t you say you were their best agent?” The words still feel strange in his mouth; he’s fallen for an international spy. Seems like the plot of a second grade romantic comedy. 

“People do this all the time. There’ll be some protocol to be followed, maybe they’ll set up security close by, but I think I’ve earned my time off.” Her fingers play with the hair at the nape of his neck and she adopts a carefree tone when she speaks next. “Besides, Ingrid is a sap, when I tell her I want to step down and take less life-risking jobs so that I can be with the man I love, there’s no way she’ll say no.”

He freezes, hands tightening around her of their own accord. She’s looking at him, unwavering, and there’s a small sound that’s close to a whimper that escapes the back of his throat without him even realizing. 

“You...what?”

“Killian Jones,” taking a deep breath, she frames his face with her hands, voice fiercely sincere, “I am in love with you.”

_ Happy _ takes on another meaning when he kisses her again. Thinks of how she’s been all around the world, and is still choosing to be here. He is surely the luckiest man alive. 

“I love you, Emma.” The words feel like relief when he says them, finally, after years of only tucking them behind his teeth. “If this is what you want, love, then this town is yours. This home. Me. All yours, as long as you’ll have them.” It’s as good as speech as any, still half-baked around the edges and he never did get to rent a boat, but with the wide smile she’s giving him, he thinks it’s enough.

She nods, curls her arms around his shoulders and nestles into his embrace. He feels Emma’s smile pressed against his skin when he kisses her hair. “Yeah,” she hums, “this is the only place I want to be.”

**Notes for the Chapter:**

> thankyou all for being along for the ride on this lil fic. drop me a comment! and come hang on [tumblr](http://piratesails.tumblr.com/) if you're so inclined!


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